Showing posts from October, 2007

Oct 2007 Dagstuhl Seminar Invitation

I have been invited to attend a Dagstuhl Seminar in May of 2008 on Graph Drawing with Applications to Bioinformatics and Social Sciences. This is a very timely event for me, as I am working with a number of grad students, namely Mike Bennett, Mike Farrugia and Eamon Phelan on just these two areas. In addition Brendan Sheehan MSc, one of my grad students, has been developing the research and method behind CellTransformer: A Tool to Generate Reaction Networks through Graph Transformation. The timing is a little tight as I need to fly to Australia shortly afterwards where I'm the Late Breaking Results Co-Chair for Pervasive 2008, the Sixth International Conference on Pervasive Computing.

I'm looking forward to hearing about work in both Bioinformatics and the Social Sciences and any new techniques and applications that are emerging.

To quote to organisers!

"Automated graph drawing deals with the layout of relational data arising from computer science (data base design, data min…

Oct 2007 Three Open Postdoc Posts

3 postdoctoral research positions available in:

* wireless sensor networks
* software engineering for autonomic systems
* enterprise systems engineering

Systems Research Group
School of Computer Science and Informatics
UCD Dublin, Belfield, Dublin 4, Ireland

The group

UCD's Systems Research Group conducts world-recognised research in
software and systems engineering, with particular emphasis on
pervasive computing, autonomic communications, software development of
dependable systems, complex systems visualisation and embedded systems
design. SRG is unique in spanning the range of systems disciplines
from hardware and programming up to mathematical modeling and
analysis, and places great emphasis on collaborative research that
leverages this expertise. The group is accommodated within UCD's
Complex and Adaptive Systems Laboratory (CASL,, a
groundbraking facility that brings together researchers in computer
science, mathematics, bioinformatics, physical and earth sci…

Oct 2007 European Patent Office Invention Filed

As part of my role as an IBM CAS Visiting Scientist I work with Extreme Blue groups during the summer period. Three of my former UCD honours student Keith, Cheryl and Darin have ended up on Extreme Blue. I consider it to be an exceptional opportunity for any grad to understand and experience industrial R&D. My involvement with Extreme Blue is a collaboration and often results in invention disclosures and from time to time a patent is filed. One such patent for a mobile recommendation invention was recently filed in Europe and we expect a follow up international application in the months to come.

Oct 2007 Tom Holland starts as IRCSET funded postgrad

I would like to welcome Tom Holland who recently started his Ph.D. with the Systems Research Group in the UCD Complex and Adaptive Systems Laboratory under my supervision with Prof. Paddy Nixon. Tom is starting his research in the area of richly sensorised pervasive computing environments. Tom has received a full scholarship from the Irish Research Council for Science, Engineering and Technology (IRCSET). He is already busy at work on the course work component of his structured PhD program, a small Ubisense location project and we have had initial contacts with an industrial partner for collaboration on his research. Tom completed his B.Sc. in Internet Computing at the University of Hull in 2006 and previously spent 3 years in commercial development roles with digital agencies in Newcastle Upon Tyne and most recently with Acknowledgement Ltd. in London. Welcome to the SRG Tom and your first paper deadline is April for UbiComp 2008!

Sept 2007 CellTransformer: A Tool to Generate Reaction Networks through Graph Transformation

Brendan Sheehan MSc, one of the PhD scholars I supervise is off to The Eighth International Conference on Systems Biology, Long Beach California Oct 1-6, 2007. He is attending various tutorials and presenting a poster on his research, namely: "CellTransformer: A Tool to Generate Reaction Networks through Graph Transformation"

Rule-based models provide a declarative means to construct a computational model of biological systems. Rules specify how the model can evolve over time by transforming the underlying data or model into its next state. Most rule-based systems operate on strings. Graph transformation systems (GTS) can provide a more direct and intuitive description of many kinds of biological data such as protein-interaction data and data relating to cell-signalling pathways. Here we implement the GTS based formalism defined by Blinov et al to help generate molecular reactions based on rules that describe interactions between protein domains. We use the GTS tool …